From 371f1d8923cd76dd1fc9da1a7a156c50d8beb616 Mon Sep 17 00:00:00 2001 From: Bastian Greshake Date: Thu, 21 Jun 2012 16:49:25 +0200 Subject: [PATCH] further work on bootstrap-variant --- .rvmrc | 2 +- Gemfile.lock | 16 ++++---- app/views/genotypes/_form.html.erb | 4 +- app/views/genotypes/index.html.erb | 2 +- app/views/index/index.html.erb | 8 ++-- app/views/layouts/application.html.erb | 39 ++++++++++--------- app/views/messages/new.html.erb | 2 +- app/views/news/index.html.erb | 14 +++---- app/views/password_resets/new.html.erb | 2 +- app/views/phenotype_comments/_form.html.erb | 2 +- app/views/phenotypes/get_genotypes.html.erb | 2 +- app/views/phenotypes/index.html.erb | 2 +- app/views/phenotypes/new.html.erb | 2 +- .../phenotypes/recommend_phenotype.html.erb | 2 +- app/views/phenotypes/show.html.erb | 6 +-- app/views/shared/_error_messages.html.erb | 2 +- app/views/shared/_warning.html.erb | 4 +- app/views/static/_disclaimer.html.erb | 2 +- app/views/static/_faq.html.erb | 2 +- app/views/users/_edit.html.erb | 4 +- app/views/users/_form.html.erb | 2 +- app/views/users/_user_is_not_user.html.erb | 2 +- app/views/users/_user_is_user.html.erb | 6 +-- app/views/users/_variations.html.erb | 2 +- app/views/users/changepassword.html.erb | 4 +- app/views/users/edit.html.erb | 4 +- 26 files changed, 71 insertions(+), 68 deletions(-) diff --git a/.rvmrc b/.rvmrc index 6d891bb..9f65225 100644 --- a/.rvmrc +++ b/.rvmrc @@ -4,7 +4,7 @@ # development environment upon cd'ing into the directory # First we specify our desired [@], the @gemset name is optional. -environment_id="ruby-1.9.2-p290@rails3" +environment_id="ruby-1.9.2-p290@opensnp" # # Uncomment following line if you want options to be set only for given project. diff --git a/Gemfile.lock b/Gemfile.lock index 3615f38..a0dd55b 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,8 +1,8 @@ GIT remote: https://github.com/norman/friendly_id.git - revision: 7ddf7ae5a23795e5d08c643c0ec68ed14bfa9e27 + revision: e39e8e0cbdf3f64350aac14ad7ece85ecf824092 specs: - friendly_id (4.0.8) + friendly_id (4.0.6) GIT remote: https://github.com/paulasmuth/recommendify.git @@ -13,7 +13,7 @@ GIT GIT remote: https://github.com/ryanb/nested_form.git - revision: 504985118c2205f36e42417e6d99cecf23385290 + revision: 1cbf61517348c701e08beea41a39f04b35115e6b specs: nested_form (0.2.1) @@ -52,9 +52,11 @@ GEM activesupport (3.0.10) archive-tar-minitar (0.5.2) arel (2.0.10) - authlogic (3.1.3) + authlogic (3.1.2) activerecord (>= 3.0.0) + activerecord (>= 3.0.7) activesupport (>= 3.0.0) + activesupport (>= 3.0.7) bartt-ssl_requirement (1.4.2) bcrypt-ruby (3.0.1) builder (2.1.2) @@ -63,7 +65,7 @@ GEM erubis (2.6.6) abstract (>= 1.0.0) escape (0.0.4) - factory_girl (3.4.2) + factory_girl (3.3.0) activesupport (>= 3.0.0) i18n (0.5.0) jquery-rails (1.0.19) @@ -84,7 +86,7 @@ GEM mime-types (1.18) mocha (0.11.4) metaclass (~> 0.0.1) - nokogiri (1.5.4) + nokogiri (1.5.3) paperclip (2.7.0) activerecord (>= 2.3.0) activesupport (>= 2.3.2) @@ -143,7 +145,7 @@ GEM archive-tar-minitar (>= 0.5.2) rubyzip (0.9.5) shoulda-context (1.0.0) - shoulda-matchers (1.2.0) + shoulda-matchers (1.1.0) activesupport (>= 3.0.0) sinatra (1.2.8) rack (~> 1.1) diff --git a/app/views/genotypes/_form.html.erb b/app/views/genotypes/_form.html.erb index 7bf2a0c..e001fb1 100644 --- a/app/views/genotypes/_form.html.erb +++ b/app/views/genotypes/_form.html.erb @@ -1,5 +1,5 @@
-
+
<%= form_for(@genotype,:html => {:class => "form-stacked", :multipart => true}) do |f| %> <%= render 'shared/error_messages', :target => @genotype %>
@@ -41,7 +41,7 @@
- <%= f.submit "Upload", :class => "primary btn" %> + <%= f.submit "Upload", :class => "btn btn-primary" %>
<% end %>
diff --git a/app/views/genotypes/index.html.erb b/app/views/genotypes/index.html.erb index b9a8df4..8299584 100644 --- a/app/views/genotypes/index.html.erb +++ b/app/views/genotypes/index.html.erb @@ -10,7 +10,7 @@ <%end%>
Python-library to parse the provided files, courtesy of Sergei Lebedev
- +
diff --git a/app/views/index/index.html.erb b/app/views/index/index.html.erb index d224721..38bc269 100644 --- a/app/views/index/index.html.erb +++ b/app/views/index/index.html.erb @@ -1,7 +1,7 @@

Welcome to openSNP

<%=image_tag "/images/microarray.png",:style => "float:left;margin: 10px"%>

-

openSNP allows customers of direct-to-customer genetic tests to publish their test results, find others with similar genetic variations, learn more about their results, find the latest primary literature on their variations and help scientists to find new associations.

Sign Up!


+

openSNP allows customers of direct-to-customer genetic tests to publish their test results, find others with similar genetic variations, learn more about their results, find the latest primary literature on their variations and help scientists to find new associations.

Sign Up!


  • For Genotyping Users
    • @@ -41,21 +41,21 @@
    -
    Search for phenotypes
    +

    Search for phenotypes

    <%=image_tag("/images/phenotypesearch.png")%> Many diseases and traits are suspected to have genetical components. Genome Wide Association Studies are a simple tool find genetic markers. Easily find people with the variation you are interested in via openSNP.

    The variation you are looking for is not entered yet? Just add it to openSNP
    -
    Easily download datasets
    +

    Easily download datasets

    <%=image_tag("/images/filedownload.png")%> The mass download-function of openSNP allows you to easily download the full genotyping raw-data in the file formats that are provided by 23andMe and deCODEme.

    As the files can be grouped by their variations for specific phenotypes it is easy to get datasets that are already usable for association studies.
    -
    Get notified about new data
    +

    Get notified about new data

    <%=image_tag("/images/rss.png")%> openSNP delivers a RSS-feed for each phenotype. So you can easily get all new datasets that get available for the phenotypes of your interest, without the need to check for new entries by hand.

    For all data junkies that need more data: There is also a feed that carries all new datasets.
    diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb index 9b9ec54..04ac2ef 100644 --- a/app/views/layouts/application.html.erb +++ b/app/views/layouts/application.html.erb @@ -33,7 +33,7 @@
      <% if current_user %>
    • - <%= image_tag current_user.avatar.url(:head),:style => "vertical-align:middle"%> <%= current_user.name %> + <%= image_tag current_user.avatar.url(:head),:style => "vertical-align:middle"%> <%= current_user.name %>
      • <%= link_to("Settings", :controller => "users", :action => "edit",:id => current_user) %>
      • <%= link_to("Edit Your Phenotypes", "/users/"+current_user.id.to_s+"/edit#phenotypes")%> @@ -56,35 +56,35 @@
        <%if current_user %> <%unless (current_user.help_one or current_user.has_sequence) && (current_user.help_two or current_user.user_phenotypes != []) && (current_user.help_three or current_user.phenotype_creation_counter != 0) == true%> -
        +
        -

        Welcome to openSNP. Here are some first steps you could do:

        +

        Welcome to openSNP. Here are some first steps you could do:

        <%if current_user.has_sequence == false and current_user.help_one == false%> -
        +
        <%=link_to(raw("×"),{:controller => "users", :action => "remove_help_one", :id => current_user},:remote => true, id: "remove_help_one", :class => "close")%> -
        Upload Your Genotyping File
        - <%=link_to(image_tag("/images/fileupload.png"), "/genotypes/new")%> +

        Upload Your Genotyping File

        + <%=link_to(image_tag("/images/fileupload.png"), "/genotypes/new")%>
        <%=link_to("Upload the genotyping raw-data you got","/genotypes/new")%> from 23andMe or deCODEme to the database of openSNP to share it with other personal genomics customers and scientists from all over the world.
        <%end%> <%if current_user.user_phenotypes == [] and current_user.help_two == false%> -
        +
        <%=link_to(raw("×"),{:controller => "users", :action => "remove_help_two", :id => current_user},:remote => true, id: "remove_help_two", :class => "close")%> -
        Enter Your Variations
        - <%=link_to(image_tag("/images/phenotypes.png"), "/users/"+current_user.id.to_s+"#unentered_variations")%> +

        Enter Your Variations

        + <%=link_to(image_tag("/images/phenotypes.png"), "/users/"+current_user.id.to_s+"#unentered_variations")%>
        Let us, and the other openSNP-users, know some of your characteristics. Like hair or eye color. Or about some diseases? <%=link_to("Whatever you feel like sharing","/users/"+current_user.id.to_s+"#unentered_variations")%>.
        <%end%> <%if current_user.phenotype_creation_counter == 0 and current_user.help_three == false %> -
        +
        <%=link_to(raw("×"),{:controller => "users", :action => "remove_help_three", :id => current_user},:remote => true, id: "remove_help_three", :class => "close")%> -
        Enter a New Phenotype
        - <%=link_to(image_tag("/images/addphenotype.png"), "/phenotypes/new")%> +

        Enter a New Phenotype

        + <%=link_to(image_tag("/images/addphenotype.png"), "/phenotypes/new")%>
        Got an idea for a phenotype that has not been asked about yet and that could have genetical roots? <%=link_to("Great, you can easily add this","/phenotypes/new")%> to the openSNP-database.
        @@ -96,28 +96,29 @@ <%end%>
        - + <% if flash[:notice] %> -
        +
        x -

        <%= flash[:notice] %>

        + <%= flash[:notice] %>
        <% end %> <% if flash[:warning] %> -
        +
        x -

        <%= flash[:warning] %>

        + <%= flash[:warning] %>
        <% end %> <% if flash[:achievement] %> -
        +
        x -

        <%= flash[:achievement] %>

        + <%= flash[:achievement] %>
        <% end %> <%= yield %>
        +

        diff --git a/app/views/messages/new.html.erb b/app/views/messages/new.html.erb index 837a707..93923f2 100644 --- a/app/views/messages/new.html.erb +++ b/app/views/messages/new.html.erb @@ -19,6 +19,6 @@

        - <%= f.submit "Send", :class => "primary btn"%> + <%= f.submit "Send", :class => "btn btn-primary"%>
        <% end %> diff --git a/app/views/news/index.html.erb b/app/views/news/index.html.erb index d11d89d..1468653 100755 --- a/app/views/news/index.html.erb +++ b/app/views/news/index.html.erb @@ -1,6 +1,6 @@

        News

        -
          +
          • On openSNP
          • New users
          • New genotypes
            • @@ -57,7 +57,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t <%=auto_discovery_link_tag(:rss,"/rss", {:title => "RSS for all genotypes"})%>

            Genotypes

            <%=link_to(image_tag("/images/rss_small.png"),"/rss")%> -
#
+
@@ -80,7 +80,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t

Users

-
# Genotype-ID
+
@@ -101,7 +101,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t

Phenotypes

-
# ID
+
@@ -119,7 +119,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t

Phenotype Comments

-
Name Variations
+
@@ -141,7 +141,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t

SNP Comments

-
Phenotype Comment By
+
@@ -163,7 +163,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t <%=link_to(image_tag("/images/rss_small.png"),"/paper/rss")%> <%=auto_discovery_link_tag(:rss,"/paper/rss", {:title => "RSS for latest publications"})%>

Latest publications

-
SNP Comment By
+
diff --git a/app/views/password_resets/new.html.erb b/app/views/password_resets/new.html.erb index a6b2033..7e4bf67 100644 --- a/app/views/password_resets/new.html.erb +++ b/app/views/password_resets/new.html.erb @@ -6,5 +6,5 @@ Fill out the form below and instructions to reset your password will be emailed <% form_tag password_resets_path do %> <%= text_field_tag "email" %> - <%= submit_tag "Reset my password", :class => "primary btn" %> + <%= submit_tag "Reset my password", :class => "btn btn-primary" %> <% end %> diff --git a/app/views/phenotype_comments/_form.html.erb b/app/views/phenotype_comments/_form.html.erb index c86c305..8a5caef 100644 --- a/app/views/phenotype_comments/_form.html.erb +++ b/app/views/phenotype_comments/_form.html.erb @@ -12,6 +12,6 @@ <%= f.text_area :comment_text, :size => "20x5" %> - <%= f.submit "Comment", :class => "primary btn" %> + <%= f.submit "Comment", :class => "btn btn-primary" %> <% end %> diff --git a/app/views/phenotypes/get_genotypes.html.erb b/app/views/phenotypes/get_genotypes.html.erb index 84f2ab1..ca11622 100644 --- a/app/views/phenotypes/get_genotypes.html.erb +++ b/app/views/phenotypes/get_genotypes.html.erb @@ -1,5 +1,5 @@

Your Download can start soon...

-
+
<%=image_tag("/images/filedownload.png",:style => "float:left")%>Our servers are working hard to deliver you a file that includes all the genotyping files of users with a variation of <%=@variation%> at the phenotype <%=@phenotype.characteristic%>.

The genotyping-files currently get zipped to lighten your download. You will receive the download-link via the eMail-address you registered your account with, as soon as the file is ready.
<%=link_to "Go Back","/phenotypes/"+@phenotype.id.to_s%> \ No newline at end of file diff --git a/app/views/phenotypes/index.html.erb b/app/views/phenotypes/index.html.erb index 83d24ef..a622f8a 100644 --- a/app/views/phenotypes/index.html.erb +++ b/app/views/phenotypes/index.html.erb @@ -1,6 +1,6 @@

Listing all Phenotypes

<%if current_user%>
<%=link_to(image_tag("/images/addphenotype_small.png",:style => "vertical-align:middle" ),:action =>"new")%> <%=link_to "The phenotype of your interest is missing? Add a new one!",:action => "new"%>
<%end%> -
SNP Author
+
diff --git a/app/views/phenotypes/new.html.erb b/app/views/phenotypes/new.html.erb index 1757654..5c1f046 100644 --- a/app/views/phenotypes/new.html.erb +++ b/app/views/phenotypes/new.html.erb @@ -29,5 +29,5 @@ -<%= f.submit :class => "primary btn" %> +<%= f.submit :class => "btn btn-primary" %> <% end %> diff --git a/app/views/phenotypes/recommend_phenotype.html.erb b/app/views/phenotypes/recommend_phenotype.html.erb index 909b82d..b4f9956 100644 --- a/app/views/phenotypes/recommend_phenotype.html.erb +++ b/app/views/phenotypes/recommend_phenotype.html.erb @@ -19,7 +19,7 @@ Below you find <%=@similar_phenotypes.size%> <%if @similar_phenotypes.size > 1%>
<%@similar_phenotypes.each do |s|%>
-
+
<%=link_to s.characteristic,s%>
Description: <%=s.description%>
diff --git a/app/views/phenotypes/show.html.erb b/app/views/phenotypes/show.html.erb index a4a2413..08863c8 100644 --- a/app/views/phenotypes/show.html.erb +++ b/app/views/phenotypes/show.html.erb @@ -25,7 +25,7 @@
-
#
+
@@ -65,7 +65,7 @@
-
User Variation
+
diff --git a/app/views/shared/_error_messages.html.erb b/app/views/shared/_error_messages.html.erb index 36e0fa6..986f5a4 100644 --- a/app/views/shared/_error_messages.html.erb +++ b/app/views/shared/_error_messages.html.erb @@ -1,5 +1,5 @@ <% if target.errors.any? %> -
+
<% target.errors.full_messages.each do |msg| %> <%= msg %>
<% end %> diff --git a/app/views/shared/_warning.html.erb b/app/views/shared/_warning.html.erb index 179129e..5cfa6bf 100644 --- a/app/views/shared/_warning.html.erb +++ b/app/views/shared/_warning.html.erb @@ -1,6 +1,6 @@
-
-
+
+

Important: Please carefully read the disclaimer on the right-hand side.

diff --git a/app/views/static/_disclaimer.html.erb b/app/views/static/_disclaimer.html.erb index 580e050..894d780 100644 --- a/app/views/static/_disclaimer.html.erb +++ b/app/views/static/_disclaimer.html.erb @@ -1,4 +1,4 @@ -
+

By signing up for openSNP you declare that you have understood the possible risks and side-effects that can occur by making your genetical and medical information available on this platform. In short:

Phenotype Number of Users
+
@@ -166,7 +166,7 @@ <% if @paginated_snp_replies != [] %>

Latest replies on your comments on SNPs

-
On Phenotype
+
diff --git a/app/views/users/_variations.html.erb b/app/views/users/_variations.html.erb index bb61f95..2d5b217 100644 --- a/app/views/users/_variations.html.erb +++ b/app/views/users/_variations.html.erb @@ -1,4 +1,4 @@ -
On SNP
+
diff --git a/app/views/users/changepassword.html.erb b/app/views/users/changepassword.html.erb index 8c55607..542b492 100644 --- a/app/views/users/changepassword.html.erb +++ b/app/views/users/changepassword.html.erb @@ -1,6 +1,6 @@

Change your email-address and password

-
+
<% # helper thing so we don't have to put up fields into every page %>
<%= form_for @user, :html => {:class => "form-stacked"} do |f| %> @@ -22,7 +22,7 @@
- <%= f.submit "Update Information",:class => "primary btn"%> + <%= f.submit "Update Information",:class => "btn btn-primary"%>
<% end %>
diff --git a/app/views/users/edit.html.erb b/app/views/users/edit.html.erb index d813156..f32831e 100644 --- a/app/views/users/edit.html.erb +++ b/app/views/users/edit.html.erb @@ -1,6 +1,6 @@
-

Edit your details

-
<%= link_to 'Back Home', current_user %>
+

Edit your details

+
<%= link_to 'Back Home', current_user %>
<%= render 'edit' %>
Characteristic Variation